I. The Use of Natural Selection to explain Chemical Behavior Raises New Questions About Natural Selection’s Actual Meaning

Purpose: This is a review of a review paper by C. de Sousa, Life As Cosmic Imperative? Phil. Trans. R. Soc. A (2011) 369, 620–623 doi:10.1098/rsta.2010.0312, and more generally, a concept known as “chemical selection.”

What is critical and central in the review paper (but more importantly to the field of chemical-origin-of-life science) is the use of “natural selection” as an underlying methodology, and if we assume that the “selection” invoked in this paper is the same interpretation of natural selection used in Cristian de Sousa’s and others, then I believe it raises new questions about what selection theory actually is. In the contexts that de Sousa and many other references (Lehninger 1980) have used it, selection is a theoretical and as yet, unproven chemical concept. It is invoked as a physical concept which in de Sousa’s words is the following:

“Selection is different. Originally formulated by Darwin as the mechanism of

evolution of reproducing living organisms, natural selection also affects replicating

molecules such as RNA, as first shown by Spiegelman [7] and since repeated

in a variety of ways by many investigators. In both cases, the essence of the

process lies in the imperfections of reproduction. For all sorts of reasons, whenever

entities are replicated, variants of the original model are inevitably produced.

Selection acts on those variants to automatically bring out those that are most

stable and, especially, most capable of producing progeny, under the prevailing

conditions. AND…” Natural selection acts blindly on the products of chance. It has no foresight.”

 

And what is interesting is that “natural selection” in de Sousa’s meaning would somehow presume to rewrite the laws of chemical behavior. It is already known that chemical reactivity is governed by chance, chance collisions of species in solution etc. and distributions of energy. But what is important from de Sousa and many other references that build on de Sousa’s “natural chemical selection model” is that it is not at all clear, what the chemical definition of natural selection actually means.  De Sousa defines natural chemical selection as a process occurring “after chemistry” in stage II.

“The first stage depended exclusively on chemistry. The second stage likewise involved chemistry, but with the additional participation of selection, a necessary concomitant of inevitable replication accidents.”

Stage II? What kind of chemical physics is this meant to be? De Sousa has no evidence for any chemical species copying themselves in nature, that is, outside of molecules derived from already extant life. A key differentiation, since his hypothesis asserts that it Stage I, “it was all chemistry”. This does not occur outside of cells, and has only been shown artificially in laboratories (i.e. PCR, rtPCR), but when these tests are done correctly they produce a negative. Should we also expect that since natural selection is falsifiable chemically it cannot be reproduced in nature, that the model of this paper also based on the same “natural selection” should meet the same burden and has been falsified by contrary laboratory results, again those actually simulating natural conditions?

If “chemical selection” is indeed a real testable theory or mechanism, as it is cited many times in peer reviewed literature, such as these, then can it be falsified? In other words, what is it about ANY chemical reaction that one can envision, that would proceed differently, WITH or WIHOUT so called the mechanisms described as natural “chemical selection?” I say that if you cannot answer that question, it does not pass muster for science. We may apply this simple test to those cases where it is claimed that “self-replication” has been confirmed in vitro, asking how the confirmed case differs from the non-confirmed case and the chemical difference(s) expected in each.

De Sousa states: “Up to this event, only chemical reactions were involved”. ..and “After

it occurred, selection was added to chemistry.” We are then to understand that something, was “added to chemistry.” And we wish to know what that something might be. If so, if one claims that this additional property exists in some cases, but not in others, how would you show that it is falsifiable? Would we expect…X…behavior of chemistry? Whatever X might be, a new reaction which selects itself towards, products? Let us write A+C-à D+E and demonstrate one example, only one, in which the chemical species proceed toward products D and E by this alleged process called “natural chemical selection.” Is there one example in all of the literature that answers this question? Again, whereby there is as he claims, a stage I and stage II. And again, de Sousa is echoing in a review, the generalized belief that this is a real phenomena. As with any real phenomena there must be falsifiable conditions, theoretical or actual, proposed in order to verify its existence. This is only one of the aspects of my objections to this paper, the other is outlined below and is more theoretical.

'Self Replicating Molecules': Why This Theory Should Be Rejected

One paper on Self Replicating Molecules [1] begins thus…“The ability to invent new materials that replicate themselves would lead to a paradigm shift in materials discovery.”  I do not doubt that. But so would the ability to invent new machines that produce more energy than they consume. That too, would revolutionize a few things as well. Sadly, neither one of these is based on solid physics, and largely this is due to the similar problems of thermodynamics.

We note that in the abstract of this paper, it is proposed to “test” virtual colloidal particles in computer simulations. And it concludes that it makes (with such computer models) such virtual colloidal particles replicate successfully. When one considers the fact that these are computer algorithms making simulated molecules, such claims are rather dubious, as to their correlation to actual physics. We note that these “molecules” themselves, are nothing but algorithms, which they’ve assigned certain rules, not unlike any other programming system, they of course must have logical rules of how the program responds. But unlike nature, how does a program “behave” differently than the experimentor expects? In theory, aren’t these results precisely what the program dictated them to be? Another very important question to ask, in my opinion is to the relevance of such models in showing anything useful, particularly since “self replicating molecules” would be expected to be real chemistry. This is after all an applied division of science, and though I’m quite familiar with computer models in chemistry, there is a very large difference here. In chemistry, one is not attempting to prove necessarily that thermodynamics might be violated. The models are based largely, on pre-existing empirically validated assumptions. These assumptions are not unlike more simplistic mathematical models of chemistry that are ubiquitous, i.e. stoichiometric laws, rate constants, and so on, that current computer models must account for.

On the other hand, there is no existing demonstrable model for self-replication of molecules. Nor are there or would there be under such circumstances, any parameters for doing so. In other words given the problem area and the circumstances facing such experimentation, are computer models not doing more to convince researchers of a possibility that doesn’t exist? For one thing, how precisely, does one “test” an output in a virtual system in an independent fashion?

I’m going to summarize and conclude the disagreements of my theory with self-replicating systems here:

http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html

Firstly, the self-replicating model presumes that the potential entropy can arbitrarily be maintained by the molecular system. In other words, it assumes that entropy can be passively removed by the system of molecules, in direct contradiction to what I propose HERE. (i.e. in a virtual closed system where the potential of S(inside) is equivalent to the potential of S(outside) in a natural system as posited by Condition I.

Secondly, they are in fact assuming a non-self replicating system in performing a computer simulation. One cannot “model” such a system by using a computer to demonstrate the production of self replicating molecules as this violates the entropic boundary. We can state that in this case, they are adding external work energy, and artificially lowering the entropy potential of the system. As I discuss in the case of machines, either perpetual energy or perpetual motion machines are forbidden in the virtual closed system of Condition I or Condition II. These results are not what would be expected. The amount of useful work energy, E^o (We have made no distinction between total potential energy here, it is net energy) that is presumably entering the system is not sufficient, i.e. E^o<< than the useful work energy required to maintain the machine against its intrinsic increase in entropy. I have defined potential entropy as the actual difference in entropy between itself and its surroundings. And though we can imagine that potential energy is being added to the system from an outside source, capable of doing work, thereby creating the impression that the entropy is being lowered) what is discovered in this model is that in the closed virtual system no work is being performed and there are specific conditions that are discussed for why this does not occur. As I further discuss in (27) HERE, we discover that there is a critical lack of any imposed resistance. Diffusion and heat loss occur passively from the energetic molecules until they reach the classic maximum entropy permitted. The problem in understanding this new theorem is defining entropy differently. Boltzmann, Schrodinger and others have defined this I believe, classically, without making exceptions to animate vs inanimate systems. We are defining this in a special case of the virtual closed system, which is a natural system without sufficient input of E^o to do useful work on the system. As we’ve said, in this case we should not expect to find a potential difference in entropy between the inside and outside of such a system, i.e. across the “entropic barrier”, as there is no means to increase or decrease the absolute entropy of a system of molecules, nor can the actively transport lower entropy into and across the barrier to reduce entropy. This is rather surprising and disagrees or contradicts with the conventional entropy definition.

 

The dictates of such a system are not the natural model, if they were, then obviously they would already know what the algorithm was for the Second Law. Obviously these are not known to  anyone. They are obviously not taking into account the entropy that is built up in their system. If they did, they would realize that it conforms to the Virtual Closed System model I’ve described recently. Regarding replication that is demonstrated, again, in computer simulations, there is perhaps, more “real” replication in a SIMS game. The “respawn” that occurs in many games is one example of perhaps “self-replication” that follows rigid programming rules and algorithms of the program, but of course no one seriously believes this has any bearing to reality. The offices that the programmers of SIMS use, likely don’t look like the Harvard physics, nor do their algorithms say they’re following some arbitrary “chemical rules”, but the way in which “Mr Sim” and “Ms Dor”,  “get together” and “replicate” is presumably based on algorithms with similar hard and logical assumptions, just like a simulator at a physics lab. Enter the variability of inputs of a player, and you have perhaps many different “unexpected” outcomes. These are no more “chemical” than the SIMS buildings are physical structures obeying the laws of engineering.

One of the presumptions of my thesis is in fact that it is not possible for such manipulations to be conducted on a system, as these directly interfere by the disruption of the input of useful energy into the system. Self replacing systems violate the “entropic barrier” of a virtual closed system, of which an inanimate system of molecules is contained, if it is truly self-contained and isolated as is assumed.

Under such conditions, they would have more chance in waiting for the spontaneous evolution of prokaryotes than of witnessing the self replication of a group of molecules. And if my theory is correct, the unexpected result is that it may be much much harder in fact, to observe a system of molecules self-replicate than the former situation, with the proviso that there is space for the evolution of higher life forms, (i.e. the virtual closed system is large enough). So allow another 3 billion years,…thus one would have to wait essentially, for an infinite amount of time. Also, if my theory is correct, we find that it might be easier to make energy and violate the first law, than to do what the proponents of self-replicating molecules propose to attempt. Where is the energy diagram, the pathway? If this theory is correct, such energy barriers might be of much greater difficulty for self replication of small groups of molecules, than for entire organisms [2].



1. Zeravcic, Z and Brenner, M Self Replicating Colloidal Structures (2013)http://www.pnas.org/content/111/5/1748.full.pdf+html
NOTE: The paper might not in fact assume a strictly closed system, however it is cited as support for theory of Self Replicating Molecules more generally, and specifically to those references I've already discussed in other blogs.
2. (see argument 5 *http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html)
3. Saccana et al (2010) http://www.physics.nyu.edu/pine/reprints/SacannaPineCOCIS2011.pdf